############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings FlowSOM_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.12.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘FlowSOM’ can be installed ... OK * used C compiler: ‘gcc (GCC) 10.3.1’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) PlotDimRed.Rd:55: Lost braces 55 | of the dimred default = function(dimred){dimred$Y}.} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PlotDimRed 81.638 0.259 82.035 FlowSOMmary 79.201 0.375 79.598 PlotOutliers 24.745 0.151 24.952 PlotMarker 22.844 0.199 23.088 UpdateMetaclusters 21.455 0.096 21.597 PlotStars 18.958 0.124 19.119 GroupStats 17.189 0.044 17.271 FlowSOM 16.867 0.111 17.016 PlotGroups 15.822 0.311 16.163 QueryMultiple 12.678 0.056 12.758 AddAnnotation 12.158 0.164 12.347 query_multiple 11.785 0.020 11.831 Plot2DScatters 10.757 0.184 10.956 PlotManualBars 10.440 0.160 10.625 GetFlowJoLabels 10.293 0.092 10.409 PlotNode 9.372 0.060 9.452 CountGroups 9.164 0.088 9.271 PlotNumbers 9.073 0.072 9.164 QueryStarPlot 9.098 0.036 9.154 PlotVariable 8.857 0.019 8.893 PlotPies 8.768 0.016 8.803 PlotFlowSOM 7.984 0.367 8.364 UpdateNodeSize 8.246 0.012 8.277 PlotLabels 7.624 0.160 7.800 SaveClustersToFCS 7.397 0.075 7.488 GetFeatures 7.379 0.012 7.404 NClusters 7.034 0.244 7.292 MetaclusterMFIs 7.112 0.119 7.246 NMetaclusters 6.936 0.167 7.118 MetaclusterCVs 6.649 0.016 6.679 TestOutliers 6.534 0.020 6.567 PlotOverview2D 6.477 0.068 6.559 GetMetaclusterCVs 6.368 0.020 6.400 GetMFIs 6.176 0.012 6.199 GetMetaclusterMFIs 6.160 0.024 6.196 GetMetaclusters 6.136 0.048 6.196 GetMetaclusterPercentagesPositive 6.174 0.004 6.190 GetPercentages 6.134 0.028 6.176 print.FlowSOM 6.072 0.040 6.125 GetCounts 5.965 0.024 6.001 GetClusters 5.899 0.044 5.956 FlowSOMSubset 5.894 0.044 5.951 GetClusterMFIs 5.872 0.040 5.925 GetClusterPercentagesPositive 5.838 0.012 5.862 NewData 5.071 0.084 5.166 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.